Microbial diversity, antimicrobial resistance and zoonotic implications of the reptile gut microbiota: an updated review

Abstract

The reptilian gastrointestinal tract harbors a complex and dynamic ecosystem of microorganisms that plays a fundamental and multifaceted role in host nutrition, immune function, and overall physiological homeostasis. This gut microbiome exhibited remarkable phylogenetic and functional diversity, intricately shaped by a confluence of host evolutionary history, dietary strategy, environmental context, captive status, and life history traits. Beyond its critical importance for reptilian health and fitness, this internal microbial reservoir is of significant and growing concern from a public health perspective, serving as a major source of zoonotic pathogens, most notably non-typhoidal Salmonella, and as a critical and underexplored hotspot for the emergence, amplification, and dissemination of antimicrobial resistance genes (ARGs), a dimension that forms the central theme of this review and is systematically examined across host ecology, captive management, and the global pet trade continuum. This comprehensive review synthesizes contemporary research on the gut microbiota across key reptilian taxa, including popular companion species such as lizards such as Eublepharis macularius and Tiliqua scincoides, snakes such as Pantherophis guttatus, Python regius and chelonians. We undertake a detailed analysis of the foundational drivers shaping microbial community structure, assembly and stability, exploring the delicate balance between core symbiotic residents, putatively beneficial probiotic candidates, and pathogenic entities. A critical and extensive focus is placed on the distribution, ecological drivers, and transmission pathways of antimicrobial resistance genes within this ecosystem, highlighting its underappreciated role in the global One Health continuum. The review further elaborates on the indispensable metabolic contributions of the microbiota to host fitness, the complex tripartite interactions involving host, microbiome and parasitic helminths or protozoa, and the implications of dysbiosis. Finally, we evaluated practical and emerging strategies for targeted microbiome modulation aimed at enhancing captive management, supporting conservation breeding outcomes, mitigating zoonotic risks and promoting sustainable herpetoculture.